Measuring the effects of an antibody response in vitro in the hopes of deciphering a correlate of protection from infection has been hampered by technical issues and limited access to a suitable set of vaccine trial clinical samples. With the conclusion of VaxGen's Phase III HIV vaccine efficacy trial in 2003, we now have the ability to refine and expand on binding and neutralization assay methods using the most unique set of clinical samples and sequence data available anywhere. Due to the large number of samples, statistical modeling for appropriate sample selection from uninfected vaccinated individuals and infected vaccinees will play a major role in Phase I. Sequence analysis using maximum likelihood estimators of positive selection of amino acid sequence data should help us identify antigenically relevant mutations that may correspond to immune escape. Novel neutralization assays are being developed at VaxGen or are commercially available from ViroLogic. Combining the selection data with these new assays should impart a significant improvement over current methods. In theory, assays that target those "hotspot" regions may more accurately predict the effects of future gp120-based vaccine candidates, creating important new tools for evaluating promising candidates.